Mercurial > repos > iuc > colibread_kissplice

annotate kissplice.xml @ 3:98734f82a87e draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 45e32ab41e7cdc4e3dabe87f074f052667c22574"
author iuc
date Wed, 22 Jan 2020 17:28:53 -0500
parents d5b4404c4788
children 7d4435f9c77d
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4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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1 <?xml version='1.0' encoding='utf-8'?>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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2 <tool profile="16.04" id="kissplice" name="KisSplice" version="2.4.0">
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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3 <description>is a local transcriptome assembler for SNPs, indels and AS events</description>
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4 <macros>
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5 <import>macros.xml</import>
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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6 </macros>
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7 <requirements>
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8 <requirement type="package" version="2.4.0p1">kissplice</requirement>
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9 </requirements>
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10 <version_command>kissplice --version</version_command>
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11 <command><![CDATA[
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12
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13 ## prepare symlinks
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14 #set $samples = ""
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16 #for x in $list_reads
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d5b4404c4788 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit 7e976e65d4630ce8b485efd1d50a168ba98276e6
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17 #set $filename = os.path.basename(str($x)) + "." + $x.ext
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18 ln -sf '${x}' '${filename}' &&
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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19 #set $samples += " -r '" + $filename + "'"
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20 #end for
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22 kissplice
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23 $samples
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24 -k ${k}
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25 -c ${c}
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26 -C ${C}
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27 ${output_context}
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28 --counts ${counts}
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29
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30 ]]></command>
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31 <inputs>
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32
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33 <param name='list_reads' argument="-r" multiple="true" format="fasta,fastq" type="data" label="Reads file" />
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34 <param argument="-k" type="integer" value="41" label="K-mer length" />
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35 <param argument="-c" type="integer" value="2" label="K-mers present strictly less than this number of times in the dataset will be discarded (integer value required)" />
4acdd256cc12 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/colibread commit a213833526146246d277ec7851165971449b501e
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36 <param argument="-C" type="float" value="0.05" label="Edges with relative coverage below this number are removed (value in [0,1) required)" />
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37 <param name="output_context" argument="--output-context" type="boolean" checked="false" truevalue="--output-context" falsevalue="" label="Output the maximum non-ambiguous context of each event" />
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38 <param argument="--counts" type="select" label="Selecting how the counts will be reported">
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39 <option value="0">Total counts</option>
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40 <option value="1">Counts on junctions</option>
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41 <option value="2">All counts</option>
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42 </param>
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43 <param name="output_option" type="select" label="Output type">
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44 <option value="alternative_file">Generate only the Alternative Splicing file</option>
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45 <option value="all_files">Generate all files</option>
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46 </param>
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47 </inputs>
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48 <outputs>
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49 <data name="type0a" format="fasta" label="Single SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0a.fa">
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50 <filter>output_option == 'all_files'</filter>
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51 </data>
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52 <data name="type0b" format="fasta" label="Multiple SNPs or sequencing errors" from_work_dir="results/*_coherents_type_0b.fa">
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53 <filter>output_option == 'all_files'</filter>
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54 </data>
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55 <data name="type1" format="fasta" label="Alternative splicing events" from_work_dir="results/*_coherents_type_1.fa"/>
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56 <data name="type2" format="fasta" label="Inexact tandem repeats" from_work_dir="results/*_coherents_type_2.fa">
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57 <filter>output_option == 'all_files'</filter>
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58 </data>
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59 <data name="type3" format="fasta" label="Short indels" from_work_dir="results/*_coherents_type_3.fa">
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60 <filter>output_option == 'all_files'</filter>
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61 </data>
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62 <data name="type4" format="fasta" label="Other events" from_work_dir="results/*_coherents_type_4.fa">
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63 <filter>output_option == 'all_files'</filter>
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64 </data>
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65 </outputs>
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66
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67 <tests>
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68 <test>
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69 <param name="list_reads" value="kissplice/reads1,kissplice/reads2" ftype="fasta" />
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70 <param name="k" value="25"/>
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71 <param name="output_option" value="alternative_file" />
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72 <output name="type1" file="kissplice/alternative_splicing.fa"/>
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73 </test>
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74 </tests>
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75
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76 <help><![CDATA[
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77
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78 **Description**
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79
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80 KisSplice is a piece of software that enables the **analysis of RNA-seq data with or without a reference genome**. It is an exact local transcriptome assembler that allows one to identify **SNPs, indels and alternative splicing events**. It can deal with an arbitrary number of biological conditions, and will quantify each variant in each condition. It has been tested on Illumina datasets of up to 1G reads. Its memory consumption is around 5Gb for 100M reads.
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81
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82 KisSplice is not a full-length transcriptome assembler. This means that it will output the variable regions of the transcripts, not reconstruct them entirely. However, KisSplice results can be further aligned to a reference transcriptome (if available), or to the output of a full-length transcriptome assembler like Trinity or Oases.
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83
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84 ------
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85
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86 **Website**
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87
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88 References, documentation and FAQ here_.
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89
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90 .. _here: http://kissplice.prabi.fr/
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93 ]]></help>
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94 <expand macro="citations">
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95 <citation type="bibtex">
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96 @article{PMID:22537044,
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97 author = {Sacomoto, G. A. and Kielbassa, J. and Chikhi, R. and Uricaru, R. and Antoniou, P. and Sagot, M. F. and Peterlongo, P. and Lacroix, V.},
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98 title = {KISSPLICE: de-novo calling alternative splicing events from RNA-seq data.},
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99 journal = {BMC Bioinformatics},
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100 year = {2012},
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101 volume = {13 Suppl 6},
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102 pages = {S5},
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103 url = {http://www.ncbi.nlm.nih.gov/pubmed/22537044},
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104 }
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105 </citation>
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106 </expand>
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107
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108 </tool>